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Yellow rust (YR) or stripe rust, caused by Puccinia striformis f. sp tritici Eriks (Pst), is a major challenge to resistance breeding in wheat. A genome wide association study (GWAS) was performed using 22,415 single nucleotide polymorphism (SNP) markers and 591 haplotypes to identify genomic regions associated with resistance to YR in a subset panel of 419 pre-breeding lines (PBLs) developed at International Center for Maize and Wheat Improvement (CIMMYT). The 419 PBLs were derived from an initial set of 984 PBLs generated by a three-way crossing scheme (exotic/elite1//elite2) among 25 best elites and 244 exotics (synthetics, landraces) from CIMMYT’s germplasm bank. For the study, 419 PBLs were characterized with 22,415 high-quality DArTseq-SNPs and phenotyped for severity of YR disease at five locations in Mexico. A population structure was evident in the panel with three distinct subpopulations, and a genome-wide linkage disequilibrium (LD) decay of 2.5 cM was obtained. Across all five locations, 14 SNPs and 7 haplotype blocks were significantly (P < 0.001) associated with the disease severity explaining 6.0 to 14.1% and 7.9 to 19.9% of variation, respectively. Based on average LD decay of 2.5 cM, identified 14 SNP–trait associations were delimited to seven quantitative trait loci in total. Seven SNPs were part of the two haplotype blocks on chromosome 2A identified in haplotypes-based GWAS. In silico analysis of the identified SNPs showed hits with interesting candidate genes, which are related to pathogenic process or known to regulate induction of genes related to pathogenesis such as those coding for glunolactone oxidase, quinate O-hydroxycinnamoyl transferase, or two-component histidine kinase. The two-component histidine kinase, for example, acts as a sensor in the perception of phytohormones ethylene and cytokinin. Ethylene plays a very important role in regulation of multiple metabolic processes of plants, including induction of defense mechanisms mediated by jasmonate. The SNPs linked to the promising genes identified in the study can be used for marker-assisted selection.

Cytogenetic and molecular studies hold significant importance in plant breeding programs. In the case of moringa, such studies are scarce. Therefore, the objective of this research was to determine the chromosomal number and genetic diversity parameters in two phenotypes of Moringa oleifera Lam. (short and long capsule) using chromosomal analysis and ISSR markers, respectively. Cytogenetic analyses were conducted using the “Somatic chromosomes in root apices” technique, with acetocarmine and papain for staining. It was possible to identify 2N = 28 chromosomes in a single cell of the long capsule phenotype, ranging in size from 0.05 to 0.10 μm. Cells in both moringa phenotypes were observed in prophase, metaphase, anaphase, and telophase. High genetic variability was found in both phenotypes of moringa, as indicated by a Shannon index of 0.81. Additionally, the principal component analysis and UPGMA (Unweighted Pair-Group Method with Arithmetic) groups revealed genetic isolation between the studied moringa phenotypes. The significant polymorphism obtained with most primers suggests that the tested ISSR markers are highly useful for studying genetic diversity in moringa. These findings provide a robust foundation for future research in genetic improvement and conservation of moringa, highlighting the relevance of cytogenetic and molecular studies in this species.

Chili pepper fruits of the genus Capsicum represent excellent experimental models to study the growth, development, and ripening processes in a non-climacteric species at the physiological, biochemical, and molecular levels. Fruit growth, development, and ripening involve a complex, harmonious, and finely controlled regulation of gene expression. The purpose of this study was to estimate the changes in transcriptome diversity and specialization, as well as gene specificities during fruit development in this crop, and to illustrate the advantages of estimating these parameters. To achieve these aims, we programmed and made publicly available an R package. In this study, we applied these methods to a set of 179 RNA-Seq libraries from a factorial experiment that includes 12 different genotypes at various stages of fruit development. We found that the diversity of the transcriptome decreases linearly from the flower to the mature fruit, while its specialization follows a complex and non-linear behavior during this process. Additionally, by defining sets of genes with different degrees of specialization and applying Gene Ontology enrichment analysis, we identified processes, functions, and components that play a central role in particular fruit development stages. In conclusion, the estimation of diversity, specialization, and specificity summarizes the global properties of the transcriptomes, providing insights that are difficult to achieve by other means.

Antecedentes: La producción de sotol ha crecido en los últimos años. Existe el interés de establecer monocultivos para mitigar la sobreexplotación de las poblaciones silvestres. Sin embargo, para un establecimiento y manejo eficiente de plantaciones es importante conocer la composición elemental de Dasylirion cedrosanum. Hipótesis: La composición mineral de Dasylirion cedrosanum refleja la composición mineral de la solución del suelo del sitio en donde crece. Especie de estudio: Dasylirion cedrosanum Trel. Sitios y años de estudio: Se muestrearon plantas y suelos durante septiembre y octubre del 2020 en San Lorenzo, Buenavista y General Cepeda, Coahuila. Métodos: Se colectaron tallos, hojas y suelos y se analizaron sus elementos. Además, se midieron caracteres morfológicos a cada espécimen. Los datos se analizaron con técnicas estadísticas multivariadas. Resultados: El Ca y N presentaron alta concentración en el suelo y en las plantas. En las tres localidades los niveles de Se fueron altos en las plantas. No obstante, el Se en la solución del suelo no fue detectable. Los individuos de San Lorenzo y General Cepeda mostraron niveles altos de Cu y Ba, a pesar de que el Cu no fue detectable en el suelo. El crecimiento mostró asociación negativa con el As, Ba, Cd, Cr, Mo, Ni y Pb y el Mg estuvo relacionado con un mayor crecimiento de Dasylirion cedrosanum. Conclusiones: Dasylirion cedrosanum dispone de mecanismos para la adquisición y concentración de los elementos de la solución del suelo, incluso cuando estos estén en concentraciones bajas.

Abstract RNA-Seq experiments allow genome-wide estimation of relative gene expression. Estimation of gene expression at different time points generates time expression profiles of phenomena of interest, as for example fruit development. However, such profiles can be complex to analyze and interpret. We developed a methodology that transforms original RNA-Seq data from time course experiments into standardized expression profiles, which can be easily interpreted and analyzed. To exemplify this methodology we used RNA-Seq data obtained from 12 accessions of chili pepper (Capsicum annuum L.) during fruit development. All relevant data, as well as functions to perform analyses and interpretations from this experiment, were gathered into a publicly available R package: “Salsa”. Here we explain the rational of the methodology and exemplify the use of the package to obtain valuable insights into the multidimensional time expression changes that occur during chili pepper fruit development. We hope that this tool will be of interest for researchers studying fruit development in chili pepper as well as in other angiosperms.

Genome–environment Associations (GEA) or Environmental Genome-Wide Association scans (EnvGWAS) have been poorly applied for studying the genomics of adaptive traits in bread wheat landraces (Triticum aestivum L.). We analyzed 990 landraces and seven climatic variables (mean temperature, maximum temperature, precipitation, precipitation seasonality, heat index of mean temperature, heat index of maximum temperature, and drought index) in GEA using the FarmCPU approach with GAPIT. Historical temperature and precipitation values were obtained as monthly averages from 1970 to 2000. Based on 26,064 high-quality SNP loci, landraces were classified into ten subpopulations exhibiting high genetic differentiation. The GEA identified 59 SNPs and nearly 89 protein-encoding genes involved in the response processes to abiotic stress. Genes related to biosynthesis and signaling are mainly mediated by auxins, abscisic acid (ABA), ethylene (ET), salicylic acid (SA), and jasmonates (JA), which are known to operate together in modulation responses to heat stress and drought in plants. In addition, we identified some proteins associated with the response and tolerance to stress by high temperatures, water deficit, and cell wall functions. The results provide candidate regions for selection aimed to improve drought and heat tolerance in bread wheat and provide insights into the genetic mechanisms involved in adaptation to extreme environments.

El hábito de crecimiento de los trigos harineros (primavera e invierno) está determinado primordialmente por el proceso de vernalización, regulado por los genes Vrn. Algunos estudios sugieren la implicación de otros genes en la diferenciación de dicha característica. Por ello, se tiene por objetivo la identificación genómica de regiones con una posible relación funcional al hábito de crecimiento. Se realizó un estudio de asociación del genoma completo (GWAS) con dos enfoques de análisis: a) FarmCPU (Unificación de Probabilidad Circulante de Modelo fijo y aleatorio) y b) BLINK (Información Bayesiana y Desequilibrio de ligamiento Anidado Iterativamente) implementados en el paquete GAPIT de R. Se utilizaron datos de 25 681 loci de polimorfismo de un solo nucleótido (SNP’s) de 7 757 colectas de T. aestivum del banco de germoplasma del CIMMYT clasificadas en cuanto a su hábito de crecimiento. Se identificaron 593 marcadores SNP’s con una alta asociación al hábito de crecimiento (p < 0.01). Pero solo 70 marcadores formaban bloques de asociación (BA) en 11 cromosomas. Como se esperaba, se identificó un BA cercano al gen Vrn1 en el cromosoma 5A. Adicionalmente se identificaron 20 regiones genómicas (BA) con asociación al hábito de crecimiento, en las que se detectó la presencia de proteínas de respuesta al estrés implicadas en procesos de aclimatación y des-aclimatación. Los resultados sugieren la participación de nuevos genes en la determinación del hábito de crecimiento en Triticum aestivum y su potencial predictivo en colectas no clasificadas.

The objective of the present work was to study the soil solution throughout time in pots under greenhouse conditions. The work consisted of monitoring the solution of calcareous soil and forest soil in the absence of plants, with different types of fertilization: treatment 1: absolute control (irrigation water); treatment 2: Steiner nutrient solution; treatment 3: solid fertilizers; and treatment 4: vermicompost tea (aqueous extract). The samples were collected weekly using lysimeters for 14 weeks. They were analyzed to determine the nitrate content, total nitrogen, calcium, potassium, magnesium, sodium, sulfur, zinc, boron, pH, electrical conductivity, and oxide-reduction potential. To understand the interactions between treatments, soil type, and time over ion behavior and availability, linear and polynomial models were used, selected by a cross-validation method, which resulted in robust models, where it was found that the pH behavior is associated with the type of fertilization and soil type, with the elapsed time being a nonsignificant factor. On the other hand, time influenced the dynamics of the remaining ions and their availability. It was found that the multiple polynomial model fit better for the variables: potassium, calcium, sodium (square degree), electrical conductivity, nitrates, sulfur (cubic degree), zinc, oxidation-reduction potential, nitrogen, magnesium, and boron (quartic degree).

Plants from arid zones of Mexico are an interesting source of phytochemicals that exhibit a large number of biological properties. In this context, Rhus microphylla (Rm) and Myrtillocactus geometrizans (Mg) fruits have been used as folk remedies and to make traditional foods, respectively; however, studies on their composition and bioactivity are limited. Thus, the objective of this work was to evaluate the yields, phenolic composition, and bioactive properties (scavenging and reducing capacities, antiproliferative, and antifungal) of aqueous and hydroalcohol extracts of Rm and Mg fruits obtained by conventional agitation and ohmic heating (OH). The results showed that the Rm fruit extracts had the highest total phenolic content (TPC) values and the strongest scavenging and reducing capacities compared to those of Mg fruits, being characterized by the presence of gallic acid, while the composition of the Mg extracts varied with respect to the extraction conditions used. Regarding antifungal activity in vitro against two phytopathogenic fungi, Rhizopus stolonifer and Fusarium oxysporum, the hydroalcohol extracts obtained by conventional agitation of both plants (RmH-C and MgH-C) showed the best inhibitory effect, respectively. Interestingly, none of the extracts under study presented cytotoxicity against the noncancerous ARPE-19 cell line, while three extracts of Rm fruit exhibited a moderate antiproliferative activity against HeLa (cancerous) cell line. These findings reveal for the first time the potential of Rm and Mg fruits as a new source of bioactive compounds for future industrial applications.

Introducción y Objetivos: Opuntia se distribuye naturalmente desde Canadá hasta Argentina, actualmente forma parte del paisaje en algunas regiones del mundo, comprende entre 191 y 215 especies; la conservación ex situ de este recurso fitogenético ha adquirido relevancia, pero la identificación de especies por semilla es una limitante cuando no se tienen caracteres morfológicos confiables. El objetivo del estudio fue caracterizar la morfología de semillas de siete especies de Opuntia e identificar caracteres morfológicos propios, para tener un criterio en la identificación de especies cuando el material vegetal conservado es semilla. M&M: Mediante la técnica de desgaste y análisis de imágenes se evaluó: grosor de testa (GT), grosor de la cubierta funicular ventral (GCFV), longitud del embrión (LE), área del embrión (AE), longitud del eje mayor (LEMA) y del eje menor (LEME). Por medio de ANDEVA exploratorios y componentes principales (CP) se detectaron los caracteres más sobresalientes. Para la clasificación y predicción de especies se realizó un análisis supervisado con los métodos K-NN y LDA. Resultados: Las diferencias en todas las variables entre especies fueron significativas. Opuntia ficus-indica presentó semillas de mayor tamaño. Las variables que más ayudan a discriminar son GCFV y GT. El análisis de componentes principales explicó el 92% de la variación total. El método de predicción K-NN, fue capaz de predecir correctamente el 83% de los casos en la clasificación de las especies. Conclusiones: Los caracteres de semillas evaluados, principalmente el GCFV y GT, pueden coadyuvar en la descripción morfológica de las especies de nopal o o en identificación de especies de Opuntia cuando sólo se tiene semilla.

Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.